Wednesday, May 30, 2012

The Evolutionary Tree Failed But Evolutionists Still Insist Evolution is a Fact

The fundamental thesis of evolution is that the species evolved according to the evolutionary tree. Students learn about the evolutionary tree in biology class and biologists use the evolutionary tree in their research. But in fact the evolutionary tree is based on a limited, and carefully selected, set of observations. Ever since Darwin, science has continued to document exceptions and anomalies—species that don’t fit neatly into the evolutionary pattern. These biological contradictions come in various forms and are found throughout the tree. For instance, species that in many regards appear to be quite similar, which evolutionists have placed on neighboring twigs of the evolutionary tree, are routinely found to have profound differences. On the other hand, species that are obviously quite different, which evolutionists have placed on distant limbs of the evolutionary tree, are often found to have profound similarities. And these various differences and similarities are found in every imaginable aspect of the species designs, ranging from the visible features of the adult form to the developing embryonic form to the underlying cellular and molecular structures. At this point, such cases are no longer exceptions and anomalies. For years evolutionists attempted to explain this growing list of contradictions using their evolutionary tree model. But it is obvious that this was an exercise in forcing the evidence to fit the theory rather than the other way around. The inexorable march of science has taken its toll and in recent years evolutionists have finally begun to deemphasize their iconic evolutionary tree model. What this does not change, however, is their insistence that evolution is a fact.

While the failure of the evolutionary tree model can be seen in data even as far back as the nineteenth century, such contradictions were generally discussed only in the highly technical scientific journals. Textbooks held to evolutionary orthodoxy and journalists dutifully reported that evolution was a scientific fact. Even today students are taught that the species fall into the expected tree pattern. But some venturesome writers are beginning to mention this unmentionable. A few years ago, for instance, the Telegraph reported that “Charles Darwin's tree of life is ‘wrong and misleading’, claim scientists.” The article reported:

They believe the concept misleads us because his [Darwin’s] theory limits and even obscures the study of organisms and their ancestries. …

Researchers say although for much of the past 150 years biology has largely concerned itself with filling in the details of the tree it is now obsolete and needs to be discarded. …

“For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.” …

More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either. …

Dr Rose said: "The tree of life is being politely buried – we all know that. What's less accepted is our whole fundamental view of biology needs to change." He says biology is vastly more complex than we thought and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.

All of this was important not because it was reporting on any new scientific findings, but rather that a fundamental failure of evolutionary theory was being reported, period. Contrary evidence was being openly discussed.

But of course none of this was allowed to cast any doubt on evolutionary theory itself. As the article reported:

"If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary – but in the past couple of years people have begun to free their minds." Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe.

It is yet another example of how well protected evolution is from the scientific evidence. The tree of life is just one of many failures of evolutionary theory. Over and over the theory fails to elucidate the science, but rather must be repeatedly modified and augmented to try to fit the data. At some point the theory becomes little more than a tautology. Whatever we discover in biology, evolution must have created it, no matter how contradictory and unlikely. The real story here is not that another prediction of evolution has failed, the real story is that evolution is protected from such failures.

82 comments:

CH: The fundamental thesis of evolution is that the species evolved according to the evolutionary tree.

Given that this tree is a prediction made by evolutionary theory, not the underlying explanation, it's unclear why we should even bother reading further.

Predictions of scientific theories are not prophecy, as they cannot take into account an infinite number of unrelated, yet parallel possible that would effect what we might observe in the future.

If they were, then scientific theories would need to include an infinite list of possible unrelated events that might effect what we observe, including yet to be conceived knowledge that hasn't been created yet.

However, scientific theories do not take this form. Nor is it clear how it would be possible to do so, as the number of exceptions would be infinite.

On the other hand, prophecy supposedly does predict what we'll experience. And it supposedly does so because it can supposedly take into account an infinite number of unrelated events since it was dictated by a supernatural being.

This is represents yet another example of a pre-elighteinment, authoritative conception of human knowledge, in that scientific theories are compared to divine communication from authoritative, supernatural beings.

That's right. There is a very strong nested hierarchy pattern. It's not perfect, but clearly not happenstance. Similarly, the Earth's orbit is clearly ellipsoid, and the imperfections can be readily explained as perturbations of the basic pattern.

Funny, the only liars I see here is you, Thorton, Zachriel and the other evolutionists who comment on this blog.

The truth is that you evolutionists have been preaching common descent for centuries. Now that common descent (hence strictly nested hierarchies) is shown to be a crock, you are accusing those who point this out of being liars? Talk about hypocrisy.

The only exception to strict common descent that Zachriel has conceded is hybridization of closely related species.

Zachriel September 13, 2010 4:48 AMLet's make a prediction: Newly discovered species, extinct or extant, will support the predicted nested hierarchy, except insofar as closely related species may occasionally hybridize. See Origin of Species for details.

So, since the tree is found to be non-nested in that distantly related species are known to have hybridized (obviously not sexually or naturally), I would hope that Zachriel would be man or woman enough to admit that evolution has been falsified.

Am I holding my breath? Nope. Evolution will once again change to claim non-observed pseudoscientific mechanisms that will supposedly explain the hybridization of distant species. Indeed, we are already witnessing the birth of cockamamie explanations such as convergent evolution and lateral or horizontal inheritance via viruses.

A good attempt(you went back a long way ),but a prediction is not a statement of fact that the tree is exclusively nested. That might take the form of" there are no exceptions to the nested hierarchy " , is it possible someone else like Dr Hunter said it?

So de point is the statistically significance of the nested hierarchy pattern against the statistically (im)probability of evolution of life. And still it would be perverse to withhold provisional assent.

velikovskys: a prediction is not a statement of fact that the tree is exclusively nested.

That's correct. It's what you do with the prediction. Here's a fuller statement on the topic from the same period:

Zachriel (June 14, 2010): "Darwin was quite aware that the phylogenetic tree was not perfect. Convergence can make it difficult to discern the tree from trait characters of the taxa, while interspecific hybridization breaks the tree structure. Furthermore, Darwin was aware that there may not be a single universal ancestor, so there could be more than one tree. Since then, many other exceptions to the phylogenetic tree have been discovered, such as endogenous retroviruses, and possibly rampant horizontal evolution at the root of the tree.

"The question, then, becomes one of how closely the actual pattern matches a tree structure. If life descended along uncrossed lines, we expect a nested hierarchy of character traits. Well, for the majority of eukaryote taxa, there is a very clear nested hierarchy (but not 100%). The evidence is less clear for bacteria, but the data suggests that even allowing for horizontal evolution, all life shares a common ancestor."

"I'd like to see a peer reviewed paper or something on the gravity of the supposed failure of the tree model for eukaryotes."

The universal ancestor - Carl WoeseExcerpt: No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.http://www.pnas.org/content/95/12/6854.full

Do orthologous gene phylogenies really support tree-thinking?Excerpt: We conclude that we simply cannot determine if a large portion of the genes have a common history.,,, CONCLUSION: Our phylogenetic analyses do not support tree-thinking.http://www.ncbi.nlm.nih.gov/pubmed/15913459

Uprooting The Tree Of Life - W. Ford DoolittleExcerpt: as DNA sequences of complete genomes have become increasingly available, my group and others have noted patterns that are disturbingly at odds with the prevailing beliefs. http://people.ibest.uidaho.edu/~bree/courses/2_Doolittle_2000.pdf

How stands the Tree of Life a century and a half after The Origin? - Maureen A O'Malley - Eugene V Koonin - July 2011Excerpt of Conclusion: The irrefutable demonstration by phylogenomics that different genes in general have distinct evolutionary histories made obsolete the belief that a phylogenetic tree of a single universal gene such as rRNA or of several universal genes could represent the “true” TOL.http://www.biology-direct.com/content/pdf/1745-6150-6-32.pdf

Guy who DOESN’T support ID: Genomics has “overturned” Darwin’s iconic Tree of LifeExcerpt: The genomics revolution, Koonin argues, … 'effectively overturned the central metaphor of evolutionary biology (and, arguably, of all biology), the Tree of Life (TOL), by showing that evolutionary trajectories of individual genes are irreconcilably different. Whether the TOL can or should be salvaged — and, if so, in what form — remains a matter of intense debate that is one of the important themes of this book. Uprooting the TOL is part of what I consider to be a ‘metarevolution,’ a major change in the entire conceptual framework of biology.'http://www.uncommondescent.com/darwinism/guy-who-doesn%E2%80%99t-support-id-genomics-has-%E2%80%9Coverturned%E2%80%9D-darwins-iconic-tree-of-life/

The Biological Big Bang model for the major transitions in evolution - Eugene V Koonin - Background: "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable; http://www.biology-direct.com/content/2/1/21

Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009Excerpt: "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. ."We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?"http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html

A New Model for Evolution: A Rhizome - Didier Raoult - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html

The "Most Productive and Influential Microbiologist in France" Is a Furious Darwin Doubter - March 2012 Excerpt: Controversial and outspoken, Raoult last year published a popular science book that flat-out declares that Darwin's theory of evolution is wrong. http://www.evolutionnews.org/2012/03/the_most_produc057081.html

Darwin's Predictions - Cornelius Hunter PhD.Excerpt: The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12]http://www.darwinspredictions.com/#_4.2_Genomes_of

Zachriel, define "statistically significant". Without a specific metric to measure what you mean by significant you wouldn't know "not significant" if you saw it. Using the "panoply of traits" is parochial if you igore genetics. The problems run deeper still because there is often incongruence between classifications based on morphology and genetics.

But at minimum, if you say "statistically significant" you must have actual numbers to back up this specific metric...

There was never any mention of statistics with regard to common descent since Darwin came up with the idea. Common descent has always been the sine qua non of evolution. This statistics tune is a new tactic by the usual prevaricators and is meant as a cover up of the fact that common descent has now been clearly falsified.

Besides, multiple inheritance has nothing to do with statistics. Either a species inherit genes/traits from multiple distant species or it does not.

To emphasize, statistics within the context of common descent is a ruse, i.e., a damn lie.

Something is statistically significant if it is unlikely to have occurred by chance. In this case, the observed nested hierarchy is more than just an artifact of happenstance, but very strongly supported. You might argue about the cause of the nested hierarchy, but you can't reasonably argue that the nested hierarchy doesn't exist or that it isn't predicted as a consequent of largely uncrossed, branching descent.

Neal Tedford: But at minimum, if you say "statistically significant" you must have actual numbers to back up this specific metric...

Theobold, A formal test of the theory of universal common ancestry, Nature 2010.

Louis , back in form. Would you suggest rubbing out the adherents of the false religion a la Elijah ?

Absolutely not. I am not Elijah. However, Elijah (or someone like Elijah) is prophesied to return soon and, if he's anything like the previous Elijah, he will be nobody's bitch. In my opinion, there is no need to rub out anybody. We all die naturally on our own anyway. The old Elijah wiped out the prophets of Baal because they were agents of discord, of disunity. Unity is righteousness. God is righteous precisely because he's ONE. Conservation of ONENESS is a karmic (spiritual) principle that not even God can break. We, too, must become ONE with God in order to live eternally.

Conservation of ONENESS is also a physical principle, the mother of all conservation principles in physics.

It does seem like objective moral good is different in the Old Testament which seems strange. You would think that being objective it would be unchanging.

Why? I don't see that. Nothing has changed. Yahweh is the same forever. So is morality.

What exactly is conservation of Oneness?

Oneness is another way of saying yin-yang. Everything comes in opposite pairs. The reason is that everything must sum up to zero or nothing. When Jesus says that he's one with the father, all he's saying is that the two are opposite pairs, master and servant.

The entire physical universe is also ONE. That is, everything adds up to nothing and any violations of oneness must be corrected one sooner or later. The corrections of violations are manifested as change/motion. Oneness is the only ontology of substance that does not lead to an infinite regress.

"But many of the upper branches, such as the mammalian branch, remain secure."

Kangaroo genes close to humansExcerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,"http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118

The Gorilla Who Broke the Tree - Doug Axe PhD. - March 2012Excerpt: Well, the recent publication of the gorilla genome sequence shows that the expected pattern just isn’t there. Instead of a nested hierarchy of similarities, we see something more like a mosaic. According to a recent report [1], “In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other…”That’s sufficiently difficult to square with Darwin’s tree that it ought to bring the whole theory into question. And in an ideal world where Darwinism is examined the way scientific theories ought to be examined, I think it would. But in the real world things aren’t always so simple.http://www.biologicinstitute.org/post/19703401390/the-gorilla-who-broke-the-tree

Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Casey Luskin - June 2011Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees)http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html

Could Chance Arrange the Code for (Just) One Gene?"our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)."http://www.creationsafaris.com/epoi_c10.htm

Chimp chromosome creates puzzles - 2004 Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in 'Nature' that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed "significant structural changes". In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, "we have seen a much higher percentage of change than people speculated." The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity. http://www.nature.com/news/1998/040524/full/news040524-8.html

Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:http://www.ncbi.nlm.nih.gov/pubmed/15716009

1. If there are cycles (parallel transfer), it is not a tree by definition from graph theory.

2. A fact is not a theory. Evolution is a theory albeit a rubbishy one, not a fact. Don't mess it up. We can talk about stat significance of correlations between predictions and observations. But "facts" are a different kettle of fish.

3. The Hamming distances between the genomes of the leaf species are so big that they fall out on the gamut of the universe, assuming gradual accumulation of mutations, rates of mutations currently observed and the age of the universe.

1. If there are cycles (parallel transfer), it is not a tree by definition from graph theory.

Yes it is, just not a 100% perfect tree. Referring to the pattern as a tree is a perfectly valid model that still is a best fit to the data by far.

2. A fact is not a theory. Evolution is a theory albeit a rubbishy one, not a fact. Don't mess it up. We can talk about stat significance of correlations between predictions and observations. But "facts" are a different kettle of fish.

That evolution - genetic and morphological changes in species through common descent over deep time - has occurred is an empirically observed fact. The theory of evolution explains the observed fact of evolution. Science has been clear of the difference between the fact and the theory since day one. However, many Creationists either through ignorance of deceit like to equivocate over the two. See the author of this blog for a prime example.

3. The Hamming distances between the genomes of the leaf species are so big that they fall out on the gamut of the universe, assuming gradual accumulation of mutations, rates of mutations currently observed and the age of the universe

Hunter's analogy between the tree of life and geocentrism is not particularly apt. One might instead compare the tree of life with the heliocentric hypothesis.

Although the heliocentric model works pretty well for our solar system, the Sun is certainly not the center of the Universe. It orbits the center of our galaxy, which in turn participates in the motion of our local cluster etc. Does that mean that we should throw away heliocentrism and with it the more sophisticated astrophysical theories, e.g. Newtonian theory of gravity? Of course not! And even Newtonian gravity has its failures such as the extra precession of Mercury's perihelion, whose explanation requires going beyond classical mechanics. Ho hum.

So when Hunter points to the latest understanding of evolution, notes the failure of the tree of life, and then wants to declare that the entire theory of evolution should be declared a failure, he just looks desperate. His audience, which consists mostly of YECs, is willing to believe his nonsense. But face it, Cornelius, you aren't even trying to win any converts, you're just preaching to the choir.

If you try to flaunt your stuff at a professional biology conference, people will shrug you off as a crackpot. And they will be right.

oleg states: "Although the heliocentric model works pretty well for our solar system, the Sun is certainly not the center of the Universe. It orbits the center of our galaxy, which in turn participates in the motion of our local cluster etc."

As to the ect. part:

The Center Of The Universe Is Life - General Relativity, Quantum Mechanics, Entropy and The Shroud Of Turin - videohttp://vimeo.com/34084462

Centrality of Each Individual Observer In The Universe and Christ’s Very Credible Reconciliation Of General Relativity and Quantum Mechanicshttps://docs.google.com/document/d/17SDgYPHPcrl1XX39EXhaQzk7M0zmANKdYIetpZ-WB5Y/edit?hl=en_US

I find it extremely interesting, and strange, that quantum mechanics tells us that instantaneous quantum wave collapse to its ‘uncertain’ 3-D state is centered on each individual conscious observer in the universe, whereas, 4-D space-time cosmology (General Relativity) tells us each 3-D point in the universe is central to the expansion of the universe. These findings of modern science are pretty much exactly what we would expect to see if this universe were indeed created, and sustained, from a higher dimension by a omniscient, omnipotent, omnipresent, eternal Being who knows everything that is happening everywhere in the universe at the same time. These findings certainly seem to go to the very heart of the age old question asked of many parents by their children, “How can God hear everybody’s prayers at the same time?”,,, i.e. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that you or I, or anyone else, should exist? Only Theism offers a rational explanation as to why you or I, or anyone else, should have such undeserved significance in such a vast universe:

Psalm 33:13-15The LORD looks from heaven; He sees all the sons of men. From the place of His dwelling He looks on all the inhabitants of the earth; He fashions their hearts individually; He considers all their works.

Moreover, the argument for God from consciousness can be framed like this:

1. Consciousness either preceded all of material reality or is a 'epi-phenomena' of material reality.2. If consciousness is a 'epi-phenomena' of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.3. Consciousness is found to have a special, even central, position within material reality.4. Therefore, consciousness is found to precede material reality.

As to the 'material' fact that, as far as the solar system itself is concerned, the earth is not 'central', I find the fact that this seemingly insignificant earth is found to revolve around the much more massive sun to be a 'poetic reflection' of our true spiritual condition. In regards to God's 'kingdom of light', are we not to keep in mind our lives are to be guided by the much higher purpose which is tied to our future in God's kingdom of light? Are we not to avoid placing too much emphasis on what this world has to offer, since it is so much more insignificant than what heaven has to offer?

Louie Giglio - How Great Is Our God - Part 2 - videohttp://www.youtube.com/watch?v=bfNiZrt5FjU

You could fit 262 trillion earths inside (the star of) Betelgeuse. If the Earth were a golfball that would be enough to fill up the Superdome (football stadium) with golfballs,,, 3000 times!!! When I heard that as a teenager that stumped me right there because most of my praying had been advising God, correcting God, suggesting things to God, drawing diagrams for God, reviewing things with God, counseling God. - Louie Giglio

"I believe in Christianity as I believe that the sun has risen. Not only because I see it, but because by it I see everything else." - C.S. Lewis

Sara Groves - You Are The Sun - Music videohttp://www.metacafe.com/watch/3993951/

Psalm 8: 3-4 When I consider Your heavens, the work of Your fingers, The moon and the stars, which You have ordained; What is man that You take thought of him, And the son of man that You care for him?

And even Newtonian gravity has its failures such as the extra precession of Mercury's perihelion, whose explanation requires going beyond classical mechanics. Ho hum.

You don't get it, Oleg. Unlike evolution, Newtonian mechanics has not changed one iota in centuries. It's still the same theory, flaws and all. Einstein never claimed that relativity is the same theory as Newtonian mechanics. No, he came up with two new theories, the special and the general theories of relativity. Newtonian physics was clearly falsified in certain domains and no physicist will deny that. Likewise, every quantum physicist worth his/her PhD knows that Einsteinian determinism is nonsense. They know that the universe is probabilistic. Does this falsify Einstein's "God does not play dice" physics? Of course it does. That's why there is a competing theory called quantum mechanics.

Evolution, by contrast, is constantly changing in order to escape falsification. Why? Because evolutionists are scared to death of falsification. They are scared because theirs is not a science but a religion.

The different theories of gravity overlap and agree in the regions where they do so. In the limit of slow velocities and weak gravitational field, Einstein's relativity agrees with Newtonian mechanics. They disagree at high velocities and strong fields, where Newtonian mechanics is not applicable.

Likewise, quantum gravity (which is not ready for prime time yet) is being built with the notion that it should agree with Einstein's relativity at long distances and times but will be different from it at short distances and times, where Einstein's theory becomes incorrect.

The same works for Darwin's early version of evolutionary theory and its later variants. Darwin said that species should form a tree of life. Modern evolutionary biologists who found the tree picture incorrect for single-celled organisms nonetheless stress that the new theory agrees with Darwin's tree of life when it comes to animals. Horizontal gene transfer is a fairly rare phenomenon in, say, mammals, and the pattern of descent is strongly dominated by the vertical signal. It's like a spider's web that connects individual tree limbs. You can take a shortcut between limbs without going through the tree, but it does not make us doubt the existence of the tree.

Basically, creationists who are desperate to avoid admitting common descent like to point to exceptions to a strict tree. Those exceptions are nevertheless other sorts of genealogy connecting the species. This they are at pains not to mention.

Then they say that a (perfect) tree has been invalidated. That leaves their audience thinking that it has been shown that there is no common descent. Which it hasn't been. They are being disingenuous.

Louis Savain said above:

There was never any mention of statistics with regard to common descent since Darwin came up with the idea. Common descent has always been the sine qua non of evolution. This statistics tune is a new tactic by the usual prevaricators and is meant as a cover up of the fact that common descent has now been clearly falsified.

Besides, multiple inheritance has nothing to do with statistics. Either a species inherit genes/traits from multiple distant species or it does not.

To emphasize, statistics within the context of common descent is a ruse, i.e., a damn lie.

There have of course been numbers of formal statistical examinations of common descent ever since the classic work of David Penny (Penny, Hendy, and Pool, Journal of Theoretical Biology, 2003). Penny has had papers on this since 1982 and he and Mike Steel have another one in 2010. Doug Theobald has taken up the subject more recently. All find strong evidence that the trees for different genes are nonrandomly similar.

So Louis Savain is totally wrong in saying that there have been no such studies. He is also totally wrong in saying that when a perfect tree is falsified, that this falsifies common descent. It falsifies one pattern of common descent.

Basically, creationists who are desperate to avoid admitting common descent like to point to exceptions to a strict tree.

Why should creationists or anybody else admit something that is so obviously a lie?

Those exceptions are nevertheless other sorts of genealogy connecting the species. This they are at pains not to mention.

That is a lie. First of all, if there are exceptions to the nested hierarchies hypothesis, then there can be no talk of common descent, can there? As anybody with two neurons between their ears can tell you, genealogy assumes common descent by definition and any exception to the rule destroys the nested hierarchies hypothesis.

Second, I am a Christian and I have no problem acknowledging that there is indeed a tree of life. The book of Genesis was the first to mention the tree of life. It is just not a tree that was arrived through common descent. It was arrived through progressive intelligent design and engineering over millions of years. Any intelligent designer who reuses previous designs must use a design hierarchy. Call it design evolution, if you wish.

Then they say that a (perfect) tree has been invalidated. That leaves their audience thinking that it has been shown that there is no common descent. Which it hasn't been. They are being disingenuous.

Wow. I don't know whether to puke or just ignore you, Felsenstein. This is pathetic. And you dare teach others? Only a logic-impaired bozo would deny that common descent necessarily implies a perfectly nested tree. If it's not perfectly nested, how can there be common descent? And you have the nerve to accuse others of being disingenuous? You are an embarrassment to the University of Washington.

[boring nonsense deleted]

I want to see papers that specifically explain how common descent can make any logical sense as a statistical phenomenon. And when you show them to me, I will tell you what to do with them in no uncertain terms.

So Louis Savain is totally wrong in saying that there have been no such studies.

I haven't seen them. I don't believe a word you say, Felsenstein. You are not worthy of being trusted. You are a liar, in my opinion, and you proved it here.

He is also totally wrong in saying that when a perfect tree is falsified, that this falsifies common descent. It falsifies one pattern of common descent.

Yeah, right. If the tree is not perfect, there can be no common descent. Put that in your pipe and smoke it. There is no such thing as a "pattern of common descent". You are making this crap up as you write. Descent is either common or it is not. Period. If is not common, it means that some form of genetic engineering occurred along the way. You may fool and brainwash your students but you don't fool everyone. Some of us can see right through your con games.

Joe Felsenstein tries to defend the use of 'statistics' and states: 'Doug Theobald has taken up the subject more recently. All find strong evidence that the trees for different genes are nonrandomly similar.'

Yet the only way Doug Theobald was able to arrive at his conclusion that statistics overwhelmingly confirmed common descent was by using the wrong null hypothesis:

Douglas Theobald's Test Of Common Ancestry Ignores Common Design - Casey Luskin December 1, 2010Excerpt: In my prior post, I explained why Doug Theobald used the wrong null hypothesis for testing common ancestry. The odds of two lengthy genes arriving at a highly similar DNA sequence by chance, or even evolutionary convergence, is extremely small. Unless there's an underlying political motive, it shouldn't take a paper in Nature to show that obvious point.,, Common descent is a much better explanation for these genetic similarities....Unless, that is, you admit the possibility of common design. If you ignore common design, then the explanation for similarities between gene sequences must be common descent. Doug Theobald's recent paper in Nature gets to his conclusion only by ignoring the possibility of common design and then equating common design (wrongly lumped with "creationism") with unguided evolutionary development -- a straw man comparison that is completely false.,,,http://www.evolutionnews.org/2010/12/douglas_theobalds_test_of_comm041071.html

Evolutionist Eugene Koonin also criticized Theobold's work:

"This experiment demonstrates that the phenomenon observed by Theobald [4] is, indeed, entirely a product of "our ability to accurately predict the sequence of a... related protein relative to an unrelated protein" regardless of the actual history of the corresponding sequences. Alignments of statistically similar but phylogenetically unrelated sequences successfully mimic the purported effect of common origin. Thus, the nature and origin of the similarity between the aligned sequences are irrelevant for the prediction of "common ancestry" of proteins under Theobald's approach. Accordingly, common ancestry (or homology, in the modern, post-Darwinian sense) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis."(Eugene V Koonin and Yuri I Wolf, "The common ancestry of life," Biology Direct, Vol. 5:64 (2010).)

further note

But Isn't There a Consilience of Data That Corroborates Common Descent? - Casey Luskin - December 2010http://www.evolutionnews.org/2010/12/but_isnt_there_lots_of_other_d041111.html

Louis Savain shows above his inability to comprehend terms like "common descent" even though he is making grand pronouncements about this. Let me give an example in simple language for him:

A tree with a loop in it (caused by hybridization) still shows common descent. All the species have a common ancestor. But because of the loop it is not a perfect tree.

As to Savain's dramatic statement that "There was never any mention of statistics with regard to common descent since Darwin came up with the idea.", I mentioned a number of papers and pointed clearly to where Savain could find one (in which journal, in which year). So what does Savain do? He says "I haven't seen them. I don't believe a word you say, Felsenstein."

It isn't a matter of belief. He can check whether these papers exist, and what they say. And he really ought to do that checking before he makes grand generalizations. Ones that are totally wrong.

Moreover Joe Felsenstein, as well as the other neo-Darwinists, when they cite 'statistics' to try to prove their atheistic version of neo-Darwinism, seem to be completely oblivious to the fact that they are using the 'logic of mathematics', logic which can't be reduced to a material basis, to try to prove that humans are purely material beings arrived at by purely material processes, and thus they are trying to prove, ultimately, that we have no transcendent mind/soul to our being. i.e. neo-Darwinists are trying, in their ill formed use of statistics, to use 'transcendent logic' to try to prove that man has no transcendent component to his being! This is an classic example of a dog pointlessly chasing his tail in a circle if ever there was one!

Mathematics is the language with which God has written the universe.Galileo Galilei

The Unreasonable Effectiveness of Mathematics in the Natural Sciences - Eugene WignerExcerpt: The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve. We should be grateful for it and hope that it will remain valid in future research and that it will extend, for better or for worse, to our pleasure, even though perhaps also to our bafflement, to wide branches of learning.http://www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html

“… if nature is really structured with a mathematical language and mathematics invented by man can manage to understand it, this demonstrates something extraordinary. The objective structure of the universe and the intellectual structure of the human being coincide.” – Pope Benedict XVI

further note:

Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer - video – (Notes in description)http://vimeo.com/32145998

Why should the human mind be able to comprehend reality so deeply? - referenced articlehttps://docs.google.com/document/d/1qGvbg_212biTtvMschSGZ_9kYSqhooRN4OUW_Pw-w0E/edit

Louis Savain shows above his inability to comprehend terms like "common descent" even though he is making grand pronouncements about this. Let me give an example in simple language for him:

A tree with a loop in it (caused by hybridization) still shows common descent. All the species have a common ancestor. But because of the loop it is not a perfect tree.

So if I crossed a Chihuahua with a Great Dane, it would be considered an exception to the nested hierarchy hypothesis and therefore, strict nested hierarchies were never a prediction of evolution? Furthermore, if identical genes are found in distantly related species, genes that could not have been obtained via hybridization, evolutionists can rest easy knowing that they never predicted strictly nested hierarchies?

Is hybridization the best excuse you guys can come up with? How lame.

AFAIC, so-called related species are not different species at all. They are just different varieties of the same species. Are Asians a different species than Caucasians? Is the mixed-race offspring of a Zulu and a Caucasian considered a hybrid of two different species?

The crux of my argument against strictly nested hierarchies is that distant branches of the tree of life are found to have similar features that could not have come about via common ancestry. Based on my conviction that the species were designed and engineered, I predict that, soon, computational analysis of various genomes will show that similar features are not just similar on the surface but are the result of complex identical sequences and even entire genes. Horizontal sequence sharing across distant species cannot be explained by conjuring up lame mechanisms such as convergence, viral vectors, etc.

As to Savain's dramatic statement that "There was never any mention of statistics with regard to common descent since Darwin came up with the idea.", I mentioned a number of papers and pointed clearly to where Savain could find one (in which journal, in which year). So what does Savain do? He says "I haven't seen them. I don't believe a word you say, Felsenstein."

It isn't a matter of belief. He can check whether these papers exist, and what they say. And he really ought to do that checking before he makes grand generalizations. Ones that are totally wrong.

You don't get it, Felsenstein. It's not that I think the papers don't exist. They may very well do. I don't trust them because they are written by evolutionists and, as we all know, evolutionists are forever trying very hard to prove something to the rest of us. Besides, these papers are almost certainly working with phylogenetic trees that are not based on actual genes but on surface similarities. Thus phylogeny is highly subjective. So yes, I can see where statistics would be a tool for the evolutionists since the classifications are not exact. But so what? The idea has always been that underneath, it's all strictly nested hierarchies. After all, bats do not breed with echolocating whales.

You realize that a Great Dane and Chihuahua are the same species? It would not be a hybrid. Coyotes and wolves have been interbreeding creating a population in the Eastern US of coyotes of unusual size.

Races are not species, bad example.

Dr Hunter makes the same point about trust in science papers, but he uses scienctific papers to discredit other papers. Why trust any? If they all are fase?

You realize that a Great Dane and Chihuahua are the same species? It would not be a hybrid. Coyotes and wolves have been interbreeding creating a population in the Eastern US of coyotes of unusual size.

Races are not species, bad example.

Wow. That's precisely my point. So-called related species are treated as different species even though they are the same species. Hybrids are not really hybrids in that sense; they're just mixed races. The visible difference between a chihuahua and a Great Dane (same species) is greater than the observed difference between a horse and a zebra. Yet zebras and horses are considered to be different species. My point is that hybrids are not really exceptions to the nested hierarchy rule.

Dr Hunter makes the same point about trust in science papers, but he uses scienctific papers to discredit other papers. Why trust any? If they all are fase?

Well, if they contradict each other, Hunter is to be commended for pointing it out.

What Louis Savain said originally, was that "There was never any mention of statistics with regard to common descent since Darwin came up with the idea."

Go that? "There never was ..." Not that there were such papers but he didn't trust them.

So I pointed out some. Then he changed his tune and said that he didn't trust them.

On the "there never was ..." issue, Savain has been shown to be totally wrong.

Awe, come on. Both you and I know that the use of statistics has nothing to do with the prediction (a purely nested tree) but with the incompleteness or uncertain nature of the phylogenetic data. Now, you and others are using it to hide the fact that you never predicted a strictly nested tree. Grow up.

Louis Savain just will not admit that he said that "there was never any mention ...". But it is evident to anyone who reads this thread that he did say that. End of story.

You are a jackass, Felsenstein. That's probably how you became a professor of evolution. You know perfectly well what I meant. The nested tree of life prediction of the theory of evolution is not and was never dependent on statistics. The statistical part came long afterwards when it became clear to the evolutionists that the phylogenetic data did not exactly match the prediction.

It takes courage to be a consequential scientist, Felsenstein. You don't have any.

Only in evolutionary arguments can you have "statistically significant" evidence without actually having statistics. That's quite a trick.

Theobald shows data that is over 20 years old before genome sequencing really became practical and showed incongruence with the morphological data. According Theobald, "It would be very problematic if many species were found that combined characteristics of different nested groupings."

“That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent."(Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution, Vol. 44, pgs. S117-S120)

'Only in evolutionary arguments can you have "statistically significant" evidence without actually having statistics. That's quite a trick.'

You're just expressing your ignorance. Many of us evolutionary biologists work on these statistical methods as our full-time jobs. I'm part of an entire lab devoted mostly to this. Go buy the book "Inferring Phylogenies" and start learning about the statistics involved.

“That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent."(Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution, Vol. 44, pgs. S117-S120)

And there are many biologists and systematists who are not particularly statistical, and thus speak about incongruence in a crude way, to later be quote-mined by creationists.

For the statistically informed, there is incongruence and incongruence. Is a measurement that says the Earth is 4.5 billion years old incongruent with a measurement that says 4.6 billion years? Well, yes and no. What we really want to know is how big is the difference?

We can now quantify the similarities and differences between phylogenetic trees. The "incongruences" between morphological and molecular phylogenetic trees within, say, mammals, can be quite interesting and important to specialists, but in the grand scheme of things they are quite minor. Google Theobald, statistics of phylogenies.

Or read the papers Felsenstein cited. You have utterly no hope of being anything other than a crank unless you read the relevant work in a field before spouting off about how it doesn't exist.

Only in evolutionary arguments can you have "statistically significant" evidence without actually having statistics. That's quite a trick.

Only on the internet can you have such a willfully ignorant blustering Creationist unwilling to do the slightest bit of research before belching out his claims.

Statistical methods like Bayesian analysis are one of the most widely used and important tools in modern genetics. Here are but three recent examples out of thousands that were easily found on Google Scholar.

Well Thorton, it is interesting that you repeatedly call people who believe in God 'ignorant' when the fact of the matter is that atheists are the ones who deny they even have a 'mind' to begin with. It can truly, and humorously, be noted that at least Theists have not 'lost their minds' as atheists have in their beliefs. ,,, But to the point of your table pounding that genetics proves neo-Darwinism true, Several studies have been listed, by fellow evolutionist themselves, which cast a high degree of doubt on your claim that genetics proves beyond any doubt that neo-Darwinism is true. Thus you have some citations and we 'ignorant' Theists also have some citations. What to do? What to do? Tell you what Thorton, let's look to see if the mechanism of neo-Darwinism, RV & NS, can be rigidly established so as to add weight to your claim that rigid proof is established for neo-Darwinism to generate the massive amounts of integrated functional information we find in life:

Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies

Where's the substantiating evidence for neo-Darwinism?https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

Hmm that's pretty weird Thorton. Not at all comforting for the rigid proof you need to make your case! Actually Thorton, the reason why neo-Darwinism will never be a adequate explanation for the massive amounts of integrated functional information we find in life is that information is its own independent and 'transcendent' entity that may be encoded onto various material mediums, but which can never be produced by material mediums: In fact that barrier to material processes is a 'law of nature' as Dr. Gitt notes at the last part of this video:

The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html

Well Thorton I did not know you were so discriminating as to which Theists you were calling ignorant. Let me guess only those Theists who agree with you that we are the result of purely undirected material processes are 'NOT" ignorant in your book? Right? Funny but I avoid such Theists as that:

2 Timothy 3:5having the appearance of godliness, but denying its power. Avoid such people.

But Thorton seeing that you, as a atheist, have 'lost your mind', i.e. that you deny the reality of your mind, even though mind is something you experience first hand, can you point me to the exact 'scientific' experiment that demonstrates consciousness 'emerges' from a material basis and does not precede material reality? Materialism simply has ZERO empirical evidence that its contention is true:

Here a Darwinian Psychologist has a moment of honesty facing the 'hard problem' that consciousness presents to materialism;

Darwinian Psychologist David Barash Admits the Seeming Insolubility of Science's "Hardest Problem"Excerpt: 'But the hard problem of consciousness is so hard that I can't even imagine what kind of empirical findings would satisfactorily solve it. In fact, I don't even know what kind of discovery would get us to first base, not to mention a home run.'David Barash - Materialist/Atheist Darwinian Psychologisthttp://www.evolutionnews.org/2011/11/post_33052491.html

Whereas the Theist's contention that consciousness/mind is a independent entity, is doing quite well empirically speaking:

Thorton, The 'hard problem' of consciousness is not a minor problem for neo-Darwinism, as even this atheistic philosopher admits:

Mind and Cosmos - Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False - Thomas Nagel - November 2012 (projected publication date)Excerpt: If materialism cannot accommodate consciousness and other mind-related aspects of reality, then we must abandon a purely materialist understanding of nature in general, extending to biology, evolutionary theory, and cosmology. Since minds are features of biological systems that have developed through evolution, the standard materialist version of evolutionary biology is fundamentally incomplete. And the cosmological history that led to the origin of life and the coming into existence of the conditions for evolution cannot be a merely materialist history.http://ukcatalogue.oup.com/product/9780199919758.do

=======

It is interesting to note that there is a very strong tradition in philosophy that holds that the most concrete thing that a person can know about reality is the fact that they are indeed conscious, i.e. that they have a 'mind':

"Descartes remarks that he can continue to doubt whether he has a body; after all, he only believes he has a body as a result of his perceptual experiences, and so the demon could be deceiving him about this. But he cannot doubt that he has a mind, i.e. that he thinks. So he knows he exists even though he doesn’t know whether or not he has a body."http://cw.routledge.com/textbooks/philosophy/downloads/a2/unit4/descartes/DescartesDualism.pdf

We even have candidate mechanisms. Not only that, but some of those mechanisms (e.g. ERVs) leave powerful evidence for common descent, simply because if an individual acquires a genetic sequence from a horizontal source, and leaves descendents, that material then provides a marker of vertical (i.e. longitudinal) inheritance patterns.

I'm not sure whether you are just wildly out of date, or deliberately misrepresenting the science.

abstract: The past 30 years have seen a revolution in comparative biology. Before that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies not only is requisite in macroevolutionarystudies but also has been applied to a wide range of topics and ﬁelds that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be-all and end-all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past —both pattern and process— is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process.